Shadow Chronicles, Remastered
by OverlordMiles
Summary: After moving from Hoenn to Orre, Dominic gets tangled into an inconceivable plot for a kid of his age. As he matures, he realizes the true intentions of others, and strives to avenge those he lost, while meeting others down the way, and aging like any other teenager would. Accepting OC's, takes place instead of the XD Gale plot. [STOPPED]
1. Confusion

**A/N: So this story is somewhat of a 'rewrite' of my previous story, The Shadow Chronicles. That was when I was a lot younger, and since I'm older and by far a better writer, I plan to make this story superior to the previous. A lot of things will be changed compared to what I made before, so if something is majorly different, don't get salty.**

 **Yeah, sorry for changing the name. xD OC form at the bottom of this chapter.**

 **Like any of my followers from that time are active anyway.**

 **Regardless of who is active or not, let's start our story. You won't miss anything if you didn't read the original.**

Dominic wearily opened his eyes, attempting to move a muscle but failing miserably. As his eyes opened to their full extent, his senses started to regain him. The first thing he noticed was pain. Everywhere. Permeating throughout all his being was a dull throb of the feeling. The second thing he noticed were bars. Iron bars were planted horizontally in front of him, each a few inches from the other. Dom made another futile attempt to move, only managing to turn his head a few degrees to the right. A steel bed with a pathetic excuse for a mattress was slung midair using two pairs of chains on the end of the bed. After painfully turning his head the other way, he noticed another steel object, this time a toilet.

 _It's so boring in here..._ Dominic thought.

After another failed attempt to get up, Dominic crawled over to one of the walls and used it to propel himself upwards. As a groggy feeling overwhelmed him, he scaled to the bars to look outside them. Down the hall were numerous other cells like his, and all of them were identical. However, the walls that weren't part of the cell had a futuristic look to them, almost like they were in some kind of alien spaceship. After looking down the hall, he looked at the cell parallel to his. Inside the cell was a familiar figure to him.

"Dad?" Dominic queried.

The figure that was sprawled out on the ground in the other cell woke up, slowly getting to a position much like Dominic's own. "Hello, son. How are you feeling?"

"Not that well. I'm really tired, like I ran a marathon!"

His father chuckled at his son's innocence.

"Well Son, I'm afraid I won't be seeing you for much longer..."

"Why is that daddy? Are you going on another vacation?"

"I guess you could call it that. Now I'm going to be gone for a long time, but I promise we'll meet again."

"What about mommy?"

"I'm going to visit her. She'll see you again when I do. Sound good?"

"Yep! You guys have fun!"

Dominic's father muttered something that he couldn't pick up.

Just then, two people in white armor with burgundy-colored cloth sticking diagonally off their helmets went up to Dominic's father's cell. They whispered some words to him, and he followed them regretfully. Dominic leaned through the bars, observing the two people as they led his dad to some unknown area. As soon as they turned, he walked over to the bed, sitting on it, and starting to think.

 _Who will take care of me when they're gone? Maybe they'll bring in the babysitter. She's nice._

Footsteps down the hallway interrupted Dom's though process. There was a person who looked the same from before, except the armor was built differently. As they talked, Dominic realized she was a girl.

"Here's your food. I'm sorry you encountered something so brutal so young, but it's beyond my power to change."

Dominic wasn't exactly sure what she meant, but gratefully took the food anyway. As he ate, he realized the food was really bland, and wherever he was was, in general, monochrome. Everything was just overall boring. The only interesting thing were the jagged blue streaks down the hallway, which occasionally lit up. He stared at them, occasionally poking some food and even more occasionally actually eating it.

* * *

 _Dominic went up to his mother, who had recently called him. He walked downstairs and confronted her face-to-face._

 _"Hey Dom... We're moving in a week. Your dad found work in another region."_

 _He was a little disappointed, because he'd be leaving his friends behind, but reluctantly agreed. He loved his mommy very much, and didn't want to anger her. In the next week, Dominic said his goodbyes, and the group left from Littleroot to a route just off Cherrygrove City, where a speedboat had reached the beach. The group, with their suitcases, boarded the ship, bounding the waves to the new region, Orre._

 _When they arrived, they looked around the lab where his father would be working. It was a modern building decked from top-to-bottom with state-of-the-art technology. Computers, screens, and the like were scattered around in a high frequency. Dom decided it would be a cool place to work if he ever grew up to be a scientist._

 _Afterwards, they moved into their two-story house in a nearby village that was less than a mile away. Only a few houses were there, ones of the people at the lab who didn't want to live there. Their house was already furnished, and although it was a bit outdated, it more than fit the family's needs. Dominic brought his suitcase up to his room (with a little help) where he settled in. The walls were a light gray color, contradicting his jet black hair. He laid back in his new bed, his jade eyes getting an excellent view of the ceilings. The room would look more interesting once he updated it. But for now, the travel had made him tired, and he fell asleep quite easily._

* * *

 _Meanwhile, back in Littleroot town, a new family moved into the house in Littleroot. A young man who would travel the region and become champion, along with his loving mother. As their truck arrived, the boy gleamed, not knowing of the adventure in front of him._

* * *

When Dominic was almost done with his meal, the same two people from before came over and asked the boy to come with them.

"Okay!" he gleamed, happy to get out of the boring containment cell. He wasn't even sure why he was in there anyway, he hadn't done anything wrong as far as he remembered. They led him into a door, where his father was. His arms and legs were stretched, held by chain. A man wearing purple came over to him, and initiated a conversation.

"Hello there! Welcome to one of the Cipher Bases. We're here to talk to you about joining. We give decent wages, free food, and starting Pokemon. Care to join?"

Dominic looked over to his father. "Only if my daddy says it's okay."

The man chuckled and flashed the boy a smile.

His father, obviously in pain, talked to him, his voice hoarse.

"Don't...do it..."

The man in purple talked to his father. "If he doesn't join, he won't be of any use to us, so we'll kill him."

Instantly, a face of fear enveloped his father's face.

"I give you consent. Do it. Just don't put down my son..."

As the man in purple ushered him out of the room with him, Dominic's father was shocked with more volts of electricity.

"I swear! I don't know anything! I just moved in here a few days ago!"

One of the men in white walked up to him. "Like we'll believe that sh*t."

* * *

Dominic was given a uniform to wear, although it was too big so they had him wear his normal clothes. Since he was not old enough to battle, they sent a man with a reasonably high stature to be his mentor. Cloaked in red and wearing a robe stood his new teacher.

"By the way, I'm a Team Cipher Admin. You may call me Snattle. Your new teacher is Eldes. Hopefully you become a good trainer so you can help us in our goal!"

"Okay!" Dominic agreed, too young to know the true nature of their plans.

And with that, Dominic was introduced to his new bunk, over the top of someone he hadn't met yet.

Little did he know what he had gotten himself into.

 **Well, that's it for the first chapter. Thoughts? Ideas?**

 **And, what most of you have been probably waiting for, OC form. Please private message me, since I don't want the review section to be clogged.**

 **Name:**

 **Age:**

 **Gender:**

 **Looks:**

 **Personality:**

 **Pokemon (Up to 3, and one Shadow max):**

 **Backstory, or any other details I may have missed:**

 **Until the next chapter!**

 **~OverlordMiles**


	2. Introductions

**Last time...**

 **-Dominic joined Cipher, as opposed to being killed.**

 **A/N Thanks for all the OC's! I may not fit them all in, but I'll do my best.**

Snattle led Dominic through the Cipher base, detailing all the rooms within the underground congregation. Snattle showed him the Grunt's Quarters, where he would be staying; the armory, where Pokemon were stored; the gym, for training Pokemon; the factory, where Shadow Pokemon were made (Snattle didn't elaborate on that for fear that Dominic would realize it was wrong); and finally, the hangar, where vehicles were stored. Snattle stated that Dominic wouldn't be using it for a while, until he was fully trusted. Finally, he led him to his bunk, where he was going to spend the night before training tomorrow.

As Dominic climbed up to his bed, his bunkmate spoke.

"They call me Dare. Who're you?"

"I'm Dominic, nice to meet you."

"Why'd you join?"

"My dad told me to."

"Must've had a damn good reason."

"Probably. They whispered some stuff to him, but I couldn't exactly hear it."

Dare put the pieces together pretty easily. He clearly didn't know the true nature of this organization, but he was in because they had some confrontation with his father, and gave him some terms or the like. After a bit, he spoke.

"When I was young, my parents dropped me off at an orphanage, with nothing but my name. After a while, I was elated to be adopted, but the family who took me was...not the most functional. After a divorce, my father won custody and took care of me, and he wasn't the best parent. He hit me a lot, and it hurt, so I ran away. I went to a different orphanage, not willing to stand against all my friends after running away, even if the family had fallen apart. I kept getting adopted, but none of the families made me feel...right. After a while, I just ran away, fending for myself. Eating scraps on the street for a month or so. Finally, a grunt encountered me and gave me an offer I couldn't refuse. And here I am."

Dominic nodded. "That's sad."

Dare looked at the wall, his hands on his knees. "How old are you kid?"

"7."

"I'm 15. They found me a year ago. They must've had a good reason for drafting a kid. You got anything special about you?"

"Not that I know."

Just then, a grunt walked in, telling them it was time to turn the lights off and at least be quiet. The two wished the other goodnight, and Dominic fell asleep quite rapidly after the eventful day.

In the morning, Dominic walked with Dare to the cafeteria, where they had biscuits and gravy. While the biscuits were very tasteless and somewhat stale, the gravy was decent and added some texture and flavor. After eating two of them, they did a role call, and Eldes came over to fetch Dominic so he could train. As he followed Eldes into the training room, he noticed Snattle talking with two other men in suits in a glass box attached to one of the walls. Eldes tossed him a Pokeball, while throwing one on the ground in front of him. Dom repeated the action, revealing that he had some kind of 'martial arts squirrel' while the opponent had some kind of 'fighting humanoid with long legs and T-Rex arms'.

Eldes gestured to his Pokemon. "This is Hitmonlee, an aggressive Fighting Type Pokemon. Your is also the Fighting Type, but it's a Mienshao. It's more defensive, and based off reading your opponent's movements. Your goal is to beat me without using a single attacking move. You will have multiple days to win, so it might be a good idea to spend your time thinking of ways to win. If you succeed, we'll move to the next challenge, and so on. Are you ready?"

Dominic nodded.

"Then let's begin! Hitmonlee, use Mach Punch!"

"Uhhh, block it!"

Mienshao crossed his arms, bracing for impact. The Hitmonlee, moving at an unbelievable pace, got a jab in where the 'X' in Mienshao's arms didn't cover. The Mienshao slid back, and after shaking off the pain, resumed to its normal spot.

"Hitmonlee, use High Jump Kick!"

Before Dom could react, Hitmonlee brought its leg down on Mienshao, fainting it.

"Good game, care to try again?"

Dom shrugged. "I got all day, apparently."

"That's the spirit."

* * *

Inside the glass box, Snattle was talking with two business representatives. The box was soundproof, so no one outside could hear.

"So why a kid?" One of the men wearing a tuxedo asked.

"Well, you see, as children develop, their minds are easily influenced. We have found a young man who is young enough for his mind to yet be sculpted, but old enough to battle successfully and carry out missions. Should this experiment succeed, we can duplicate it multiple times with different cases. Soon, we will create a generation of soulless monsters without even a tinge of remorse to back it up. These will be the 'Perfect Cipher Grunts' I've been working on. As they influence their Shadow Pokemon, they will be harder to purify, unlike what Wes did 5 years ago."

The other man spoke. "It's a Farfetch'd idea, but it could potentially work. Send us reports as your experiment progresses, and we'll soon consider whether or not to invest in your trade."

After Snattle escorted the two men out, Dominic and Eldes left the room, since Dominic was tired out after getting beaten so many times. An hour or two later, dinner was called, and Dominic met with Dare again. As Dom slowly ate his food, Dare noticed how visibly tired Dom was.

"Man, what did they make you do? Run a marathon?"

Dominic sighed. "They gave me a really tough battle, and I'm stumped on what to do..."

"What is it? Maybe I could help."

"Well I have a Mienshao, and I gotta beat a Hitmonlee without using attacking moves. Any suggestions?"

"This could be a long shot, but I'm pretty sure Mienshaos would know Detect and Counter. Detect is like protect, and Counter deals damage back to the opponent after being hit."

Just then, everything clicked in Dominic's mind. "Thanks a lot, I think I got it now."

After the two retired to their rooms, they talked a little bit about their pasts, and then fell asleep before curfew.

* * *

 _Dominic was woken up from his slumber when he heard a scream from downstairs. He climbed downwards, and was face to face with a man in with armor._

 _"Hey little guy! We're gonna take care of you now, okay?"_

 _Just then, a dart was planted into his arm. Suddenly, he felt tired, even though he just slept. Consciously slipped away from him, and the last thing he saw before falling into the man's arms was his mother sleeping on the table, a pool of red liquid sitting placidly around her. His eyes shut, temporarily removing him from reality. The man in armor sent the sleeping figure back to his colleagues, who hauled it into the back of their truck. They then stormed the house until they found Dominic's dad in his office, with the door locked._

 _"Sir, open up."_

 _After no response, they decided to threaten him._

 _"Sir, we have your son. Please comply or this will be his last day of sunlight."_

 _Then, the door opened, and the man in a white lab coat threw his hands up. They forcefully tugged him into the truck, putting duct tape over his mouth so he couldn't scream. Then, the truck started, and they were off._

* * *

The next morning, right after breakfast, Dominic followed Eldes back to the training room. Snattle sat in his chair, watching as the battle unfolded. As soon as Hitmonlee used Mach Punch, Dominic had Mienshao use Counter. The Mach Punch struck, but Mienfoo hit back harder. Hitmonlee was slightly dazed, but shook it off as it was commanded to use High Jump Kick.

"Detect!"

Time seemed to slow down as Mienshao used Detect. It evaluated its surroundings, sensing for threats. As it felt the Hitmonlee charging at him, it readied itself to spring. As soon as the Hitmonlee came near, Mienshao leaped out of the way, leaving Hitmonlee to dig its heel into dust, the impact temporarily crippling it. It moaned in pain before it fainted.

"Excellent job. We may now progress your training." Eldes stated, a hint of happiness in his voice.


	3. Realization

**Thanks for all the support this story is getting. Then again, I mostly write in the Homestuck fandom, and this has so many more people.**

 **Without further ado, story!**

As Dominic walked back to his bunk, he found Dare already sitting on the bed, reading a book.

"Good evening, Dare."

"Hey man, I have something serious to talk to you about. We need to go somewhere private."

"Where did you have in mind?"

A few minutes later, the two were locked in a unisex bathroom that was the furthest from the center of activity. After locking the door, Dare started telling Dom what could only be described as the truth.

"Look Dom, it's about time I tell you. Cipher is a criminal organization. They're not trying to make the world better, they're trying to overrun it. Probably 70% of the crap they've told you is bullsh*t. You didn't necessarily have a choice joining, but you have a chance now. To be honest, I'm done with this place. I don't necessarily care about what happens with the rest of my life, because I've already ruined it. You, you however have a chance."

Dom hesitantly nodded. _Can I believe this guy? He has been my bunkmate for half a year... I'll consider what he has to say._

"What I'm saying is, I want you to escape. If I do too, well then that's an added bonus. I'm kind of impartial at this point though. I believe you can be something greater, better than some tool for this corrupted organization. You can be your own man, not someone else's puppet. How much have they told you about Shadow Pokemon?"

"Well, to be honest... Not much."

"Exactly. They're trying to keep the truth from you. A year or two from now, you would've trusted them so much that their beliefs would've been law to you. No one would be able to convince you otherwise. You would be their pawn. You want free will? This is the only way. If we wait too long, it'll be too late. Are you in?"

Dominic paused for a moment. _If I had to be honest with myself... I trust Dare more than Eldes. Yes, he's my mentor, but... I can feel the emotion in his words. The genuine feel to his statement... He's really fighting for what he wants._

"I'll do it."

"Really?"

"Yeah. I'm a bit hesitant, but... I trust you."

"Awesome! Let me tell you the plan. Remember, if I fall, keep treading. This is about you."

* * *

Right after dinner, Dominic walked up to the armory.

"Woah, what's this?"

A scientist came up to him. "You're probably someone's kid. This is the armory. We store our weapons here."

"Cool, can I see some?"

"Well, I guess it can't hurt. You can't stop a child's curiosity, can you?"

The scientist detailed each of the weapons, explaining them and their practical uses.

"And this is a taser. You use it if you want to stun someone, but not kill them. Useful for capture missions."

As the scientist turned to walk to the next one, Dominic plucked it right off the display.

"Hey kid, put that back. It's not safe for a chi-"

Dominic pushed the trigger, releasing a magnitude of volts into his body.

"Fascinating..." he said, taking some other weapons and hiding him in his coat. Then, he stomped loudly (that being the signal), and caught Dare as he walked by the door, staging the weapon handoff as an accidental collision, they said their 'Sorrys' and continued to the next stage of the plan.

Dominic walked to the bunks, preparing for 'a good night's sleep'.

* * *

As Dare reached the security office, he strangled the guard outside, slowly letting him down to the ground. He walked through the sliding doors, shooting the two people watching the monitors with a salvaged tranquilizer gun. He then set the footage of the room with their bunk with one from a previous night, making sure the alarm wouldn't go off from the sudden motion detection. After taking the unconscious guard outside into the room, shooting him with a dart just to be safe, he left so the plan could continue.

* * *

The next part of the plan would have to be timed decently between the two members of the escape group if they were to make it out successfully. While everyone thought they were asleep, Dare and Dom split off, where Dare went to the hangar while Dom went to the Pokemon Storage Room. Since he didn't have a Pokemon of his own, he was to steal one, or a few for purification. Dare was to open the hangar to make a clean escape. Dare hastily took out the guards with dual tasers, preparing to open the ramp to the desert above. He hovered by the control panel, waiting for Dom to come. If he took too long, someone would notice, since the hangar was the only way in and out of the complex, as far as the grunts knew.

* * *

Dominic made it to the storage room without much trouble, scanning the room until he found some decently powerful Pokemon to take before he met up with Dare and escaped. As he got around 10 Pokeballs and put them in his satchel, he turned around to find himself face-to-face with a woman.

"Your smile is so cute... I wonder what would happen if I were to, say, burn it off?"

The girl gave a maniacal laugh, reaching to her belt for a Pokeball.

"I'm Crimson Gordin, remember the name for as long as you live, which probably won't be long, considering you're committing treason to Orre's biggest criminal organization."

Dominic chuckled himself. "How about no."

Before Crimson could throw out a Pokemon to battle, he pulled out a Pokeball of his own.

"Electabuzz, use Thunder Wave!"

As soon as the young adult was hit with the zap of the thunder type move, her body froze as she fell to the ground.

"God damn... Beaten, by a kid... I'll get you for this!"

Of course, it sounded a lot less threatening considering she could hardly talk.

After returning the humanoid Pokemon to its home, he ran past the teenager and searched his mental map for the hangar. After finding a quick route, he slid down the rails of a staircase, making a few turns through the hallways before running into the hangar, where Dare was waiting. As Dare saw Dom run into the room, he laughed, pulling the lever to open the hangar. Dom ran into the front section of a motorcycle, letting Dare get in the side compartment. Dom revved the engine, and they drove up the concrete ramp into the desert beyond.

* * *

As they made it more than a mile from the base, they slowed down the motorcycle, cruising at a constant pace. Dare started talking.

"I was skeptical on whether that would work or not but, damn, that just happened."

"Yeah, but at least now I know th-"

A loud sound rang through the open expanse of the desert, followed by a cry of pain from Dare. Dom looked back to find Crimson, the girl from earlier, trailing them on a smaller and more agile motorcycle. After looking at Dare, and the hole through his chest, he decided that stunning wouldn't work anymore. He pulled a pistol from his satchel, taking a few shots. The first hit the sand harmlessly. The second hit the hull of the motorcycle, making the vehicle shudder from impact but continue at the same pace. The third one grazed her shoulder, making her cry in pain but continue driving. The final shot in the clip hit the back wheel, making the motorcycle frontflip, crushing her from the impact. Once the two were out of range, Dom stopped the motorcycle and went up to Dare.

"You okay man?"

"To be honest...No..."

"What do you mean you're not okay?"

"I think... My time is over. I'm gonna die..."

"No! You can't!"

"I'm going to. It's inevitable. Just accept it and it'll be less pain..."

"There's gotta be something I can do..."

"It hit my lungs. I can hardly talk..."

"Then don't! I can get you to a hospital!"

"I'd rather use my last words...to tell you..."

"Tell me what?!"

"My real name... is Derek... Just promise you'll avenge me..."

"I will... I'm sorry I couldn't have done anything..."

"Don't feel bad...about...it..."

Just then, Dominic almost felt his body go limp, the pulse disappearing from his body. Dominic put his body back in the side compartment, driving the motorcycle away as tears cascaded down his face.


	4. Quick Author's Note

**Quick Author's Note:**

 **(This will be deleted once the new chapter comes out.)**

 **I haven't updated this story in quite a while (two weeks, actually) because I'm finishing up my other story, Exodus. If you like Homestuck, please check it out.**

 **Anyway, as soon as I finish the story, I'll put extra effort into this story to make up for the current inactivity.**

 **Thanks for understanding! Until the next chapter!**

 **~OverlordMiles**


End file.
